{"id":"https://openalex.org/W4323670171","doi":"https://doi.org/10.1515/jib-2022-0054","title":"SBML level 3 package: spatial processes, version 1, release 1","display_name":"SBML level 3 package: spatial processes, version 1, release 1","publication_year":2023,"publication_date":"2023-03-01","ids":{"openalex":"https://openalex.org/W4323670171","doi":"https://doi.org/10.1515/jib-2022-0054"},"language":"en","primary_location":{"id":"doi:10.1515/jib-2022-0054","is_oa":true,"landing_page_url":"https://doi.org/10.1515/jib-2022-0054","pdf_url":"https://www.degruyter.com/document/doi/10.1515/jib-2022-0054/pdf","source":{"id":"https://openalex.org/S4393917359","display_name":"Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics","issn_l":"1432-4385","issn":["1432-4385","1613-4516"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Integrative Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"diamond","oa_url":"https://www.degruyter.com/document/doi/10.1515/jib-2022-0054/pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5027644564","display_name":"James C. Schaff","orcid":"https://orcid.org/0000-0003-3286-7736"},"institutions":[{"id":"https://openalex.org/I140172145","display_name":"University of Connecticut","ror":"https://ror.org/02der9h97","country_code":"US","type":"education","lineage":["https://openalex.org/I140172145"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"James C. Schaff","raw_affiliation_strings":["University of Connecticut , Storrs , CT , USA"],"raw_orcid":"https://orcid.org/0000-0003-3286-7736","affiliations":[{"raw_affiliation_string":"University of Connecticut , Storrs , CT , USA","institution_ids":["https://openalex.org/I140172145"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020061602","display_name":"Anuradha Lakshminarayana","orcid":null},"institutions":[{"id":"https://openalex.org/I140172145","display_name":"University of Connecticut","ror":"https://ror.org/02der9h97","country_code":"US","type":"education","lineage":["https://openalex.org/I140172145"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Anuradha Lakshminarayana","raw_affiliation_strings":["University of Connecticut , Storrs , CT , USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Connecticut , Storrs , CT , USA","institution_ids":["https://openalex.org/I140172145"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061773929","display_name":"Robert F. Murphy","orcid":"https://orcid.org/0000-0003-0358-901X"},"institutions":[{"id":"https://openalex.org/I74973139","display_name":"Carnegie Mellon University","ror":"https://ror.org/05x2bcf33","country_code":"US","type":"education","lineage":["https://openalex.org/I74973139"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Robert F. Murphy","raw_affiliation_strings":["Carnegie Mellon University , Pittsburgh , PA , USA"],"raw_orcid":"https://orcid.org/0000-0003-0358-901X","affiliations":[{"raw_affiliation_string":"Carnegie Mellon University , Pittsburgh , PA , USA","institution_ids":["https://openalex.org/I74973139"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076617999","display_name":"Frank Bergmann","orcid":"https://orcid.org/0000-0001-5553-4702"},"institutions":[{"id":"https://openalex.org/I223822909","display_name":"Heidelberg University","ror":"https://ror.org/038t36y30","country_code":"DE","type":"education","lineage":["https://openalex.org/I223822909"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Frank T. Bergmann","raw_affiliation_strings":["University of Heidelberg , Heidelberg , Germany"],"raw_orcid":"https://orcid.org/0000-0001-5553-4702","affiliations":[{"raw_affiliation_string":"University of Heidelberg , Heidelberg , Germany","institution_ids":["https://openalex.org/I223822909"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008451312","display_name":"Akira Funahashi","orcid":"https://orcid.org/0000-0003-0605-239X"},"institutions":[{"id":"https://openalex.org/I203951103","display_name":"Keio University","ror":"https://ror.org/02kn6nx58","country_code":"JP","type":"education","lineage":["https://openalex.org/I203951103"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Akira Funahashi","raw_affiliation_strings":["Keio University , Yokohama , Japan"],"raw_orcid":"https://orcid.org/0000-0003-0605-239X","affiliations":[{"raw_affiliation_string":"Keio University , Yokohama , Japan","institution_ids":["https://openalex.org/I203951103"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011118845","display_name":"Devin P. Sullivan","orcid":"https://orcid.org/0000-0001-6176-108X"},"institutions":[{"id":"https://openalex.org/I86987016","display_name":"KTH Royal Institute of Technology","ror":"https://ror.org/026vcq606","country_code":"SE","type":"education","lineage":["https://openalex.org/I86987016"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Devin P. Sullivan","raw_affiliation_strings":["KTH-Royal Institute of Technology , Stockholm , Sweden"],"raw_orcid":"https://orcid.org/0000-0001-6176-108X","affiliations":[{"raw_affiliation_string":"KTH-Royal Institute of Technology , Stockholm , Sweden","institution_ids":["https://openalex.org/I86987016"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5067339679","display_name":"Lucian P. Smith","orcid":"https://orcid.org/0000-0001-7002-6386"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Lucian P. Smith","raw_affiliation_strings":["University of Washington , Seattle , WA , USA"],"raw_orcid":"https://orcid.org/0000-0001-7002-6386","affiliations":[{"raw_affiliation_string":"University of Washington , Seattle , WA , USA","institution_ids":["https://openalex.org/I201448701"]}]}],"institutions":[],"countries_distinct_count":4,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5067339679"],"corresponding_institution_ids":["https://openalex.org/I201448701"],"apc_list":null,"apc_paid":null,"fwci":1.1996,"has_fulltext":true,"cited_by_count":8,"citation_normalized_percentile":{"value":0.78459791,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":99},"biblio":{"volume":"20","issue":"1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.996399998664856,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.996399998664856,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9944000244140625,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11829","display_name":"Mathematical Biology Tumor Growth","score":0.9495000243186951,"subfield":{"id":"https://openalex.org/subfields/2611","display_name":"Modeling and Simulation"},"field":{"id":"https://openalex.org/fields/26","display_name":"Mathematics"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/sbml","display_name":"SBML","score":0.9913274049758911},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7898114919662476},{"id":"https://openalex.org/keywords/encode","display_name":"ENCODE","score":0.5669644474983215},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.4731895923614502},{"id":"https://openalex.org/keywords/markup-language","display_name":"Markup language","score":0.43700796365737915},{"id":"https://openalex.org/keywords/core","display_name":"Core (optical fiber)","score":0.4287196397781372},{"id":"https://openalex.org/keywords/core-model","display_name":"Core model","score":0.423348605632782},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.40631043910980225},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.113575279712677},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.09028187394142151},{"id":"https://openalex.org/keywords/xml","display_name":"XML","score":0.0779029130935669}],"concepts":[{"id":"https://openalex.org/C87186988","wikidata":"https://www.wikidata.org/wiki/Q452197","display_name":"SBML","level":4,"score":0.9913274049758911},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7898114919662476},{"id":"https://openalex.org/C66746571","wikidata":"https://www.wikidata.org/wiki/Q1134833","display_name":"ENCODE","level":3,"score":0.5669644474983215},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.4731895923614502},{"id":"https://openalex.org/C45874996","wikidata":"https://www.wikidata.org/wiki/Q37045","display_name":"Markup language","level":3,"score":0.43700796365737915},{"id":"https://openalex.org/C2164484","wikidata":"https://www.wikidata.org/wiki/Q5170150","display_name":"Core (optical fiber)","level":2,"score":0.4287196397781372},{"id":"https://openalex.org/C2780366209","wikidata":"https://www.wikidata.org/wiki/Q5170200","display_name":"Core model","level":2,"score":0.423348605632782},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.40631043910980225},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.113575279712677},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.09028187394142151},{"id":"https://openalex.org/C8797682","wikidata":"https://www.wikidata.org/wiki/Q2115","display_name":"XML","level":2,"score":0.0779029130935669},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C76155785","wikidata":"https://www.wikidata.org/wiki/Q418","display_name":"Telecommunications","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1515/jib-2022-0054","is_oa":true,"landing_page_url":"https://doi.org/10.1515/jib-2022-0054","pdf_url":"https://www.degruyter.com/document/doi/10.1515/jib-2022-0054/pdf","source":{"id":"https://openalex.org/S4393917359","display_name":"Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics","issn_l":"1432-4385","issn":["1432-4385","1613-4516"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Integrative Bioinformatics","raw_type":"journal-article"},{"id":"pmh:oai:pubmedcentral.nih.gov:10063174","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10063174","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10063174/pdf/jib-20-1-jib-2022-0054.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Integr Bioinform","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:f53a158868fc4ed9861524443532f67a","is_oa":true,"landing_page_url":"https://doaj.org/article/f53a158868fc4ed9861524443532f67a","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Integrative Bioinformatics, Vol 20, Iss 1 (2023)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1515/jib-2022-0054","is_oa":true,"landing_page_url":"https://doi.org/10.1515/jib-2022-0054","pdf_url":"https://www.degruyter.com/document/doi/10.1515/jib-2022-0054/pdf","source":{"id":"https://openalex.org/S4393917359","display_name":"Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics","issn_l":"1432-4385","issn":["1432-4385","1613-4516"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Integrative Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320321114","display_name":"Bundesministerium f\u00fcr Bildung und Forschung","ror":"https://ror.org/04pz7b180"},{"id":"https://openalex.org/F4320330124","display_name":"German Network for Bioinformatics Infrastructure","ror":null},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320334764","display_name":"Japan Society for the Promotion of Science","ror":"https://ror.org/00hhkn466"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4323670171.pdf"},"referenced_works_count":18,"referenced_works":["https://openalex.org/W74322794","https://openalex.org/W239577987","https://openalex.org/W1525863646","https://openalex.org/W1998801111","https://openalex.org/W2040890820","https://openalex.org/W2102653059","https://openalex.org/W2107062718","https://openalex.org/W2114124738","https://openalex.org/W2123756340","https://openalex.org/W2131067724","https://openalex.org/W2150908245","https://openalex.org/W2163493106","https://openalex.org/W2169509065","https://openalex.org/W2284531492","https://openalex.org/W2988361147","https://openalex.org/W6630086920","https://openalex.org/W6675376083","https://openalex.org/W6966240955"],"related_works":["https://openalex.org/W2134221731","https://openalex.org/W2465447782","https://openalex.org/W4295136412","https://openalex.org/W4281744058","https://openalex.org/W4225469991","https://openalex.org/W2602804230","https://openalex.org/W1989258321","https://openalex.org/W4226414617","https://openalex.org/W2123928201","https://openalex.org/W4323670171"],"abstract_inverted_index":{"Abstract":[0],"While":[1],"many":[2],"biological":[3],"processes":[4,16,32,58,108],"can":[5],"be":[6,29],"modeled":[7],"by":[8],"abstracting":[9],"away":[10],"the":[11,22,73,91,105],"space":[12,26],"in":[13,35,59],"which":[14],"those":[15],"occur,":[17],"some":[18],"modeling":[19],"(particularly":[20],"at":[21],"cellular":[23],"level)":[24],"requires":[25],"itself":[27],"to":[28,53,71,94,97],"modeled,":[30],"with":[31],"happening":[33],"not":[34,48],"well-mixed":[36],"compartments,":[37],"but":[38,62],"spatially-defined":[39],"compartments.":[40],"The":[41,81],"SBML":[42,69,82,87],"Level":[43,88],"3":[44,89],"Core":[45,74],"specification":[46,75],"does":[47,64],"include":[49],"an":[50],"explicit":[51],"mechanism":[52,67],"encode":[54,98],"geometries":[55,99],"and":[56,76,100,107],"spatial":[57,102],"a":[60,66],"model,":[61],"it":[63,109],"provide":[65],"for":[68,86],"packages":[70],"extend":[72],"add":[77],"additional":[78],"syntactic":[79],"constructs.":[80],"Spatial":[83],"Processes":[84],"package":[85],"adds":[90],"necessary":[92],"features":[93],"allow":[95],"models":[96],"other":[101],"information":[103],"about":[104],"elements":[106],"describes.":[110]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":2}],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-10-10T00:00:00"}
